Pull List Specifications

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Changes since last version

Quality Control Functionality

Design Specification
Section Change Reason for change

Version: 1.1

Outstanding issues and omissions

Section Issue or Ommission

Distribution control
Author:
Shelley Tworoger
Owner and approver for
distribution: Shelley Tworoger
Signature: Date:

Brigham and Women’s Hospital, Channing Laboratory

Copyright © 2005. All rights reserved.

Author: Shelly Tworoger Page 1 of 12 Date: 24/12/2008

Pull List Specifications

Distribution List
Company Entity Recipient Name Action

Shelley Tworoger

Mark Magid
Rakesh Kukatla
Helena Judge-Ellis
Jeanne Sparrow
Eric Rimm
Sue Hankinson

Author: Shelly Tworoger Page 2 of 12 Date: 24/12/2008

Pull List Specifications

Contents

1. Introduction 4
1.1 Purpose of document................................................................................4
1.2 Background................................................................................................4
1.3 Scope of the specification.........................................................................4
1.4 Input 4
1.5 Output 5
1.6 Glossary of Terms and Definitions.............................................................7
1.7 Contacts9
1.7.1 List of comments of final sign off............................................................9

2. Functional Overview...............................................................................10
2.1 Business Objectives
(See separate, expanded flow chart for sorting)............................................10
2.2 .a Functional Diagram.............................................................................10
2.2.b Functional Diagram in more detail.......................................................11
“Original Sort List”
instructions to go from pulled order to aliquot order.......................................11
“Sending Sort List”........................................................................................11
2.3 Design Mock-up.......................................................................................12
2.4 Requirements..........................................................................................12
2.4.1 Primary.................................................................................................12
2.5 Non-Functional Requiremets...................................................................12
2.6 Outstanding Issues..................................................................................12

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1.Introduction

1.1Purpose of document
The Quality Control (QC) Functionality will continue the process of pulling samples
from the freezer and ultimately sending to a laboratory. This functionality will build on
the information generated in the Pull List and Sorting Functionalities, specifically
identifying and placing QC and drift samples into a project going to a laboratory. The
purpose of this document is to outline the specifications for the QC functionality in
HealthTrack.

1.2Background
QC samples are an important aspect of any biospecimen project. These samples,
which are split samples from the same individual or pool of individuals, allow the
research to estimate the quality of the assay being conducted on regular study
participant samples. QCs only apply to actual projects being sent to a laboratory, not
to samples being placed back into the freezer repository. The purpose of this project
will be to create an application as part of HealthTrack that will allow the research
assistant to identify the type and number of QCs needed for a project and for
HealthTrack to place the QC samples into specific box positions and create a QC info
file mapping real QC ID to a fake ID. This functionality will be integrated within the
sorting functionality.

1.3Scope of the specification

The concern of this application and specification is the integration of QC selection and
placement into the Sorting Functionality. A completed pull list is a requirement to any
work within this application.

1.4Input
QC functionality input data comprises of:

• The number of QCs as a percent of the total number of participant samples

being sent out.

• Set size of QCs. This defines how many QCs will be placed next to each other
as a “set” – this is to make QC samples indistinguishable from normal
participant samples. This field should allow multiple selection from 1 to 6.

• Type of QC. This defines which QCs will be used and is based on the QC type
table that will be developed based on the Excel file “List of QC Types and
cohorts.xls”. This field should allow multiple selection. NOTE for genetics
projects where we use real participant sample for QCs, the user will select

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“39”, which denotes genetic QCs. The study coordinator and RA will then
make the QC file matching real ID to fake ID to input directly into GenT, using
the fake IDs chosen for the supposed “39” pool of QCs.

1.5Output
Primary output – QC Info File
The QC info file contains the information about QC type, fake IDs and the location of
each QC in the box. The QC Types are chosen by the user. The fake ID and location
in the box are assigned by HealthTrack as follows:
• Given the number of QCs as a percent of the total sample size (n), the set
sizes (s, t, etc.), and the selection of QC types (x, y, etc.), there will
approximately an equal number of each set size; the types of QCs will be
approximately evenly distributed across sets (a set has all of one type of QC).
For example for a 1000 sample project with 10% QCs, the total number of
QCs will be 100. If the user chooses set sizes of 2 and 3, there will be 20 QC
sets of size 2 and 20 QC sets of size 3. If the user chose QC type “37” and
“38” then there will be 10 QC sets of size 2 and 10 QC sets of size 3 using
“37” and 10 QC sets of size 2 and 10 QC sets of size 3 using “38”.
• For each QC sample, a fake ID will be chosen and assigned to that sample.
The fake ID should have the same format as the study participant IDs in the
project – hence the fake IDs are cohort specific. A list of possible fake IDs that
do not overlap with any real participant IDs for each cohort will be a table in
the database.
• QC samples will be assigned locations in boxes based on the set size(s)
selected by the user. For example, if set size 2 and 3 are chosen, than an
some QC samples will be included in the boxes as a set of 2 and others as a
set of 3. These sets should be evenly distributed throughout the boxes within a
lab code.
• A QC info file needs to be generated to report all the above information to the
user. The QC info files will have four variables: Fake QC ID, Box Location, QC
type, and labcode (sorted by labcode and then box locations).
FAKE BOX QC LAB
QC ID LOC TYPE CODE
----------- ---------- ----------- ----------
275205A 1(6,5)50 3700000 1
1314484 1(6,6)51 3700000 1
2347176 1(6,7)52 3700000 1

3384074 2(2,1)10 3800000 1

3446464 2(2,2)11 3800000 1
1244101 2(2,3)12 3800000 1

1597001 3(3,1)19 postqc1 2

1705931 3(3,2)20 postqc1 2
2396912 3(3,3)21 postqc1 2

2386574 4(2,1)10 postqc2 2

2757926 4(2,2)11 postqc2 2
343136A 4(2,3)12 postqc2 2
• A label file, containing the labels using the Fake IDs will be generated to

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match the labels made for the real study samples.

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1.6Glossary of Terms and Definitions

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Term Definition
Assay Any type of measurement done on a biological sample
A oracle view that combines fields from a normalized structure of
Translation Table many fields to create one long but shallow table of permutations that
can be used in the UI for user’s ease
Vial A tube filled with biological specimen to be used in an assay request
or as part of a pull list.
General term for the functionality that generates the all the vial lists
Pull List including freezer locations, used to pull biospecimens from freezers
for a set of labcodes.
STAGES OF PULL LIST
Entering the initial data for a pull list, choosing labcodes, setting
Initialization parameters. Includes making decisions about appropriate parameter
settings and changing those parameters to get the best list. Vials are
temporarily reserved until the parameters are changed or approved.
Approved and finalized the pull list, all final parameter settings
selected. Vials are reserved in the database. Pull list has been
Active (Activate) generated and blood lab personnel are actively pulling samples out
of the freezer. Includes updating the freezer file when an incorrect
tube is found, getting new locations of alternate vials, and noting
what new subvials have been created.
Completed and After all vials have been pulled for a particular pull list, updates are
Updated made to the freezer file, including marking of original vials (and
subvials) as removed. Also includes final update to the sub-sending
list that notes which vials were sent for which assay requests.
TYPES OF LISTS IN PULL LIST FUNCTIONALITY
Original vial list List of original vials, separated by vial type (i.e. vial size), with
locations in the freezer and other information (see appendix) to be
used for pulling vials for a Pull List. Generated by the pull list
functionality.
Subvial list List of subvials, separated by assay request, with locations in the
freezer and other information (see appendix) to be used for pulling
vials for a Pull List. Generated by the pull list functionality.
Index number A sequential set of numbers, beginning at 1, assigned to each vial in
a pull list overall all original and sub-vial lists. In other words, no
number is repeated and this acts as a unique identifier within pull
list.
Unique Vial ID ID number assigned by oracle for every vial handled in a pull list or
other project
Participant ID The ID number assigned to a participant when he or she entered the
study
Pull list ID ID number assigned by oracle for each Pull List generated for a set
of assay requests.
Sub-sending list A list of all potential IDs/vials in an assay request. Notes what vial
was sent for that individual, whether a vial was sent for that
individual, and if not sent then why.
Original Sort List A set of instructions, with list of original vials (separated by vial
type/size), their locations in the Freezer Pull Box and their new

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1.7Contacts
Name Job Title/ Position/ Signoff Telephone E-mail
Role
Shelley Project Lead 5-2087 nhsst@channing.ha
Tworoger rvard.edu
Mark Magid Project 5-0074 mgmagi@hotmail.c
Development om
Rakesh Project 5-2575 rkukatla@hsph.harv
Kukalta Development ard.edu
Helena Lab Manager 617-732-5781 nhhje@channing.ha
Judge Ellis rvard.edu
End User
Jeanne Data Manager 5-4220 nhjms@channing.h
Sparrow arvard.edu

1.7.1List of comments of final sign off

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2.Functional Overview
2.1Business Objectives
(See separate, expanded flow chart for sorting)
2.2.a Functional Diagram
Enter Assay Request
*if replace/delete participants
**if need to change parameters
***if a vial is
missing in
freezer, pull
alternate vial if
one exists, if Generate Sub-Sending List by Assay Request
not remove from
list + any matched
controls if a case
-Aliquot sort list, separated
by original vial volume
-Generates labels for newly
aliquoted tubes
Actual aliquots recorded
in healthtrack
New aliquots into
sending box
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Enter Assay Request Enter Assay Request
Conduct tally to find cases/controls
that may need to be removed,
update sending lists.
Create Pull List Request
* **
See Intermediate Results (Put “hold” on potential vials)
Finalize Pull List
Generate Freezer Pull List(s)
Generate Pull Box Labels
(Blood Lab RA Pulls Tubes***)
to note which ID’s will actually be set.
Sorting Lists Information Defined (e.g. Box size, aliquot volumes)
Sort Lists Generated
Final sort list, separate by assay
request , notes where subvials are
placed into sending boxes. Make
QC labels
Add QCS w/ labels that have fake ID’s
Put subvials into
sending box
Computer generates a box list/ASCII file
Double check, give sub-sending list to programmer
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2.2.b Functional Diagram in more detail

Sorting
“Freezer Pull Box” “Freezer Pull Box”
Originals Subvials

“Original Sort List”

instructions to go from pulled
order to aliquot order

“Original Sort Box”

Originals sorted into aliquot order,
(CaCo order) within vial type,
before aliquotting

“Sending Sort List”

Instructions to go from aliquot order
“Aliquot “Aliquot
Store Box” Send Box” (originals) or from pulled order (subs) to
Subvials, Subvials,
aliquotted aliquotted sending order
from originals from originals
for permanent for lab codes. “Final Sending Box”
storage. Requires
Requires Aliquot Sheet All subs to send out sorted into
Aliquot Sheet

QC vials added to
Storing Final Sending Boxes

“Permanent Storage Box” Double check:

Subs not sent out, put in new o vials against boxlist
locations, recorded in Htrack o ID list (ascii file) against boxlist

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2.3Design Mock-up
2.4Requirements

2.4.1Primary

Below are the fields that should be included on the QC Request user-interface (which will
reside in the Sort Functionality):

Percent QC - User entered number that is the percent of the total number of
samples in a project.

Set size of QCs - Multiple selection simple table with choices of 1 through 6.

Type of QC - Multiple selection simple table (Use all columns describing QC pool).

2.5Non-Functional Requiremets
Research Assistants and Lab Technicians are not typically technically advanced. The
user interface of this and any part of Htrack needs to accommodate for their skill set
and ensure usability by making the product as easy to use for non-technical people
as possible.

2.6Outstanding Issues
None.

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